7Y19 | pdb_00007y19

Transcriptional regulator BrpR

PDB DOI: https://doi.org/10.2210/pdb7Y19/pdb

Classification: TRANSCRIPTION
Organism(s): Vibrio vulnificus CMCP6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-07 Released: 2023-07-05
Deposition Author(s): Ki, N., Ha, N.C., Seung-Ho, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.291 (Depositor), 0.300 (DCC)
R-Value Work:
0.221 (Depositor), 0.230 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for the biofilm regulation of transcription factor BrpR in Vibrio vulnificus

Ki, N., Seung-Ho, H.

To be published.

Macromolecule Content

Total Structure Weight: 16.32 kDa
Atom Count: 1,039
Modeled Residue Count: 132
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator VpsR	A	144	Vibrio vulnificus CMCP6	Mutation(s): 0 Gene Names: VV1_0525
UniProt
Find proteins for A0A3Q0L274 (Vibrio vulnificus (strain CMCP6)) Explore A0A3Q0L274 Go to UniProtKB: A0A3Q0L274
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3Q0L274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.291 (Depositor), 0.300 (DCC)
R-Value Work: 0.221 (Depositor), 0.230 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.259	α = 90
b = 53.259	β = 90
c = 143.926	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.